Structure of IDP90657

2.25 Angstrom resolution crystal structure of UDP-N-acetylmuramate--L-alanine ligase (murC) from Yersinia pestis CO92 in complex with AMP

Edit deposit information
CSGID target
IDP90657 
PDB Id
4HV4 (NCBI MMDB
Authors
A.S.Halavaty,G.Minasov,I.Dubrovska,J.Winsor,L.Shuvalova,S.Peterson,W.F.Anderson,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Andrei Halavaty 
Responsible lab
Northwestern University 
Deposition Date
Nov 05, 2012 
Release Date
Nov 21, 2012 

Annotation

Description
The crystal structure of UDP-N-acetylmuramate-L-alanine ligase (murC) from Yersinia pestis CO92 in complex with AMP was determined by molecular replacement and refined to 2.25 A resolution. Two chains (1.0 A r.m.s.d. over 458 C-alpha atoms) in the P212121 asymmetric unit do not bury significant surface area to be classified as a dimer according the PISA analysis. Crystal packing did not revealed any reliable oligomers too. Each copy of the protein consists of three domains with each domain represented by a central beta-sheet that is flanked by alpha helices. The N-terminal domain has a parallel 5-stranded beta-sheet, whereas middle and C-terminal domains have antiparallel 10-stranded and 6-stranded, respectively, beta-sheets. The N-terminal domain is the smallest of the three domains. Molecule of adenosine monophosphate is bound at the interface between the middle domain and the C-terminal domain. The electron density of the ligand is well resolved.  
Functional assignment
Ligase 

Ligands

Ligand code Name Ligand type
AMP biological
175 3,5-dihydro-5-methylidene-4h-imidazol-4-on

Structure information

Unit cell parameters

Space Group
P 21 21 21  
Unit Cell

a=66.53Å, b=78.02Å, c=183.30Å
α=90.00, β=90.00, γ=90.00 
Solvent content
 
Matthews coefficient
 

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
29.70-2.25Å (2.31-2.25Å)  
Rall(%)
18.2 
Rwork(%)
17.9 (20.6) 
Rfree(%)
22.4 (27.3) 
Num. observed reflections
45828 (3329) 
Num. Rfree reflections
2337 (179) 
Completeness(%)
99.3 (98.3) 

Model parameters

Num Atoms
7256  
Num Waters
282  
Num Hetatoms
346  
Model mean isotropic B factor
31.200Å2  
RMSD bond length
0.012Å  
RMSD bond angle
1.589°  
Filename uploaded
4HV4.pdb (uploaded on Jun 04, 2015 3:55 PM)  
Inserted
Nov 05, 2012